The Kobo will respect the settings within the book with regard to margins (and line spacing). You will need to strip these in Calibre (or by hand-editing) if they're hard-coded.
The space at the bottom may be partially because of the default widows and orphans setting which can create a larger space at the bottom under certain conditions. Again, you can adjust this within the book - check the forum using those keywords for specific instructions.
Not sure about it not holding the brightness setting, as I've not seen that before (except with the 1% light bug, which doesn't apply) - that sounds like a glitch to me. You may have to reset in order to fix it?
Check your Reading Settings: you can adjust tap zones in various ways.
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